Contacts of the strand formed by residues 106 - 112 (chain A) in PDB entry 1HKC


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with HIS 106 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ARG      5.2     1.6    -      -       -      -
     96A  GLN*     2.7    56.5    +      -       +      +
     98A  ASN*     5.2     1.2    +      -       -      -
    104A  ASN      4.5     0.2    +      -       -      -
    105A  VAL*     1.3    77.3    -      -       -      +
    107A  MET*     1.3    82.2    +      -       -      +
    108A  GLU*     3.8    21.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  LEU*     3.9    26.7    -      -       -      -
     94A  ARG      3.3    13.9    -      -       -      +
     95A  VAL*     3.7    15.9    -      -       +      -
    105A  VAL*     4.2     4.9    +      -       +      +
    106A  HIS*     1.3    91.4    +      -       -      +
    108A  GLU*     1.3    62.4    +      -       -      +
    109A  SER*     5.9     0.4    -      -       -      -
    216A  THR*     6.0     0.2    -      -       +      -
    446A  GLU*     6.0     4.5    -      -       +      -
    447A  SER*     4.5    13.9    -      -       -      +
    448A  GLY      6.0     0.2    -      -       -      +
    451A  LYS*     3.4    49.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ILE      4.0     0.2    -      -       -      +
     93A  LEU*     3.1     3.9    -      -       -      +
     94A  ARG*     2.8    50.6    +      -       +      +
    106A  HIS*     3.8    18.8    +      -       +      +
    107A  MET*     1.3    76.1    -      -       -      +
    109A  SER*     1.3    61.6    +      -       -      +
    137A  PHE*     4.5     2.3    -      -       +      -
    141A  ARG*     2.6    44.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ARG*     4.5    15.7    +      -       -      +
     92A  ILE      3.2     6.5    -      -       -      -
     93A  LEU*     3.6    28.9    -      -       -      -
    107A  MET*     5.9     0.4    -      -       -      -
    108A  GLU*     1.3    77.2    -      -       -      +
    110A  GLU*     1.3    68.5    +      -       -      +
    111A  VAL*     5.4     3.1    -      -       -      +
    137A  PHE*     4.8     2.2    -      -       -      -
    141A  ARG*     5.0     2.3    +      -       -      -
    447A  SER*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ARG*     3.1     1.7    -      -       -      -
     92A  ILE      2.7    36.9    +      -       -      -
    109A  SER*     1.3    79.0    -      -       -      +
    111A  VAL*     1.3    66.9    +      -       -      +
    112A  TYR*     3.4    32.6    +      -       +      -
    137A  PHE*     4.1     8.3    -      -       +      -
    140A  LYS*     3.2    28.4    -      -       -      -
    141A  ARG*     2.7    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  SER*     3.5    32.3    -      -       -      +
     90A  PHE      3.4     8.5    -      -       -      +
     91A  ARG*     3.9    20.4    -      -       +      +
    109A  SER*     5.4     3.6    -      -       -      +
    110A  GLU*     1.3    81.0    -      -       -      +
    112A  TYR*     1.3    71.6    +      -       -      +
    113A  ASP*     4.1     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  PHE*     2.8    30.2    +      +       +      +
     92A  ILE*     3.5    34.1    -      -       +      -
    110A  GLU*     3.4    35.6    +      -       +      -
    111A  VAL*     1.3    79.5    -      -       -      +
    113A  ASP*     1.3    65.4    +      -       -      +
    114A  THR*     3.4     9.7    +      -       -      -
    133A  CYS*     3.5    45.8    -      -       +      -
    136A  ASP*     3.1    20.4    +      -       -      -
    137A  PHE*     2.8    36.4    -      -       +      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il